FHIR Genomics Implementation Guide

Notice

Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.

StructureDefinition UKCore-Procedure

Used for detailing information on procedures the patient has had performed, to aid interpretation of Genomic test results.

Assertion of an absence of a procedure being performed SHOULD be recorded using an Observation resource, as described in Profile-UKCore-Observation

At a minimum, Procedure resources are expected to contain the status, code, subject and performedDateTime, though additional information conforming to the FHIR profile below MAY be included if relevant.

Genomic Study and Genomic Study Analysis profiles on Procedure may also be used as part of structured reporting. Mandated usage of these profiles is pending data standard discovery work to identify the items required within Genomic Test Reporting. As such, elements called out, and guidance suggested on this page, may be subject to change.

Profile url	FHIR Module	Normative Status
https://fhir.hl7.org.uk/StructureDefinition/UKCore-Procedure	UKCore	trial-use

UKCoreProcedure (Procedure)	I		Procedure	There are no (further) constraints on this element Element id Procedure Short description An action that is being or was performed on a patient Definition An action that is or was performed on or for a patient. This can be a physical intervention like an operation, or less invasive like long term services, counseling, or hypnotherapy. Data type Procedure Constraints dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources `contained.contained.empty()` dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated `contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()` dom-3: If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource `contained.where((('#'+id in (%resource.descendants().reference \| %resource.descendants().as(canonical) \| %resource.descendants().as(uri) \| %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()` dom-6: A resource should have narrative for robust management text.`div`.exists() dom-5: If a resource is contained in another resource, it SHALL NOT have a security label `contained.meta.security.empty()` Mappings rim: Entity. Role, or Act workflow: Event rim: Procedure[moodCode=EVN]
id	Σ	0..1	string	There are no (further) constraints on this element Element id Procedure.id Short description Logical id of this artifact Definition The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes. Comments The only time that a resource does not have an id is when it is being submitted to the server using a create operation. Data type string
meta	Σ	0..1	Meta	There are no (further) constraints on this element Element id Procedure.meta Short description Metadata about the resource Definition The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource. Data type Meta Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A
implicitRules	Σ ?!	0..1	uri	There are no (further) constraints on this element Element id Procedure.implicitRules Short description A set of rules under which this content was created Definition A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc. Comments Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc. Data type uri Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a
language		0..1	codeBinding	There are no (further) constraints on this element Element id Procedure.language Short description Language of the resource content Definition The base language in which the resource is written. Comments Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource. Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute). Data type code Binding A human language. CommonLanguages (preferred) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a
text		0..1	Narrative	There are no (further) constraints on this element Element id Procedure.text Short description Text summary of the resource, for human interpretation Alternate names narrative, html, xhtml, display Definition A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety. Comments Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a "text blob" or where text is additionally entered raw or narrated and encoded information is added later. Data type Narrative Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: N/A rim: Act.text?
contained		0..*	Resource	There are no (further) constraints on this element Element id Procedure.contained Short description Contained, inline Resources Alternate names inline resources, anonymous resources, contained resources Definition These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope. Comments This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels. Data type Resource Mappings rim: Entity. Role, or Act rim: N/A
extension	I	0..*	Extension	There are no (further) constraints on this element Element id Procedure.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
modifierExtension	?! I	0..*	Extension	There are no (further) constraints on this element Element id Procedure.modifierExtension Short description Extensions that cannot be ignored Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). Requirements Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
identifier	Σ	0..*	Identifier	There are no (further) constraints on this element Element id Procedure.identifier Short description External Identifiers for this procedure Definition Business identifiers assigned to this procedure by the performer or other systems which remain constant as the resource is updated and is propagated from server to server. Requirements Allows identification of the procedure as it is known by various participating systems and in a way that remains consistent across servers. Comments This is a business identifier, not a resource identifier (see discussion). It is best practice for the identifier to only appear on a single resource instance, however business practices may occasionally dictate that multiple resource instances with the same identifier can exist - possibly even with different resource types. For example, multiple Patient and Person resource instances might share the same social insurance number. Data type Identifier Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CX / EI (occasionally, more often EI maps to a resource id or a URL) rim: II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT] servd: Identifier workflow: Event.identifier w5: FiveWs.identifier v2: Some combination of ORC-2 / ORC-3 / OBR-2 / OBR-3 / IPC-1 / IPC-2 / IPC-3 / IPC-4 rim: .id
instantiatesCanonical	Σ	0..*	canonical(PlanDefinition \| ActivityDefinition \| Measure \| OperationDefinition \| Questionnaire)	There are no (further) constraints on this element Element id Procedure.instantiatesCanonical Short description Instantiates FHIR protocol or definition Definition The URL pointing to a FHIR-defined protocol, guideline, order set or other definition that is adhered to in whole or in part by this Procedure. Comments see Canonical References Data type canonical(PlanDefinition \| ActivityDefinition \| Measure \| OperationDefinition \| Questionnaire) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a workflow: Event.instantiatesCanonical rim: .outboundRelationship[typeCode=DEFN].target
instantiatesUri	Σ	0..*	uri	There are no (further) constraints on this element Element id Procedure.instantiatesUri Short description Instantiates external protocol or definition Definition The URL pointing to an externally maintained protocol, guideline, order set or other definition that is adhered to in whole or in part by this Procedure. Comments This might be an HTML page, PDF, etc. or could just be a non-resolvable URI identifier. Data type uri Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a workflow: Event.instantiatesUri rim: .outboundRelationship[typeCode=DEFN].target
basedOn	Σ I	0..*	Reference(CarePlan \| ServiceRequest)	There are no (further) constraints on this element Element id Procedure.basedOn Short description A request for this procedure Alternate names fulfills Definition A reference to a resource that contains details of the request for this procedure. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(CarePlan \| ServiceRequest) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) workflow: Event.basedOn rim: .outboundRelationship[typeCode=FLFS].target[classCode=(various e.g. PROC, OBS, PCPR, ACT, moodCode=RQO].code
partOf	Σ I	0..*	Reference(Procedure \| Observation \| MedicationAdministration)	There are no (further) constraints on this element Element id Procedure.partOf Short description Part of referenced event Alternate names container Definition A larger event of which this particular procedure is a component or step. Comments The MedicationAdministration resource has a partOf reference to Procedure, but this is not a circular reference. For example, the anesthesia MedicationAdministration is part of the surgical Procedure (MedicationAdministration.partOf = Procedure). For example, the procedure to insert the IV port for an IV medication administration is part of the medication administration (Procedure.partOf = MedicationAdministration). Data type Reference(Procedure \| Observation \| MedicationAdministration) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) workflow: Event.partOf rim: .inboundRelationship[typeCode=COMP].source[classCode=SBADM or PROC or OBS, moodCode=EVN]
status	S Σ ?!	1..1	codeBinding	Element id Procedure.status Short description A code specifying the state of the procedure. Definition A code specifying the state of the procedure. Generally, this will be the in-progress or completed state. Comments The "unknown" code is not to be used to convey other statuses. The "unknown" code should be used when one of the statuses applies, but the authoring system doesn't know the current state of the procedure. This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid. Data type code Binding A code specifying the state of the procedure. EventStatus (required) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a workflow: Event.status w5: FiveWs.status rim: statusCode
statusReason	Σ	0..1	CodeableConcept	There are no (further) constraints on this element Element id Procedure.statusReason Short description Reason for current status Alternate names Suspended Reason, Cancelled Reason Definition Captures the reason for the current state of the procedure. Comments This is generally only used for "exception" statuses such as "not-done", "suspended" or "aborted". The reason for performing the event at all is captured in reasonCode, not here. Data type CodeableConcept Binding A code that identifies the reason a procedure was not performed. ProcedureNotPerformedReason(SNOMED-CT) (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD workflow: Event.statusReason rim: .reason.Observation.value
category	Σ	0..1	CodeableConcept	There are no (further) constraints on this element Element id Procedure.category Short description Classification of the procedure Definition A code that classifies the procedure for searching, sorting and display purposes (e.g. "Surgical Procedure"). Comments Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. Data type CodeableConcept Binding A code that classifies a procedure for searching, sorting and display purposes. ProcedureCategoryCodes(SNOMEDCT) (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD w5: FiveWs.class rim: .outboundRelationship[typeCode="COMP].target[classCode="LIST", moodCode="EVN"].code
code	S Σ	0..1	CodeableConceptBinding	Element id Procedure.code Short description A code identifying the procedure performed. Alternate names type Definition The specific procedure that is performed. Use text if the exact nature of the procedure cannot be coded (e.g. "Laparoscopic Appendectomy"). Requirements 0..1 to account for primarily narrative only resources. Comments Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. Data type CodeableConcept Binding A code from the SNOMED Clinical Terminology UK. UKCoreProcedureCode (preferred) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD workflow: Event.code w5: FiveWs.what[x] v2: OBR-44/OBR-45 rim: .code
subject	S Σ I	1..1	Reference(Patient \| Group)	Element id Procedure.subject Short description Who the procedure was performed on. Alternate names patient Definition The person, animal or group on which the procedure was performed. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Patient \| Group) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) workflow: Event.subject w5: FiveWs.subject[x] v2: PID-3 rim: .participation[typeCode=SBJ].role w5: FiveWs.subject
encounter	Σ I	0..1	Reference(Encounter)	There are no (further) constraints on this element Element id Procedure.encounter Short description Encounter created as part of Definition The Encounter during which this Procedure was created or performed or to which the creation of this record is tightly associated. Comments This will typically be the encounter the event occurred within, but some activities may be initiated prior to or after the official completion of an encounter but still be tied to the context of the encounter. Data type Reference(Encounter) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) workflow: Event.context w5: FiveWs.context v2: PV1-19 rim: .inboundRelationship[typeCode=COMP].source[classCode=ENC, moodCode=EVN]
performed[x]	S Σ	0..1		Element id Procedure.performed[x] Short description When the procedure was performed. Definition Estimated or actual date, date-time, period, or age when the procedure was performed. Allows a period to support complex procedures that span more than one date, and also allows for the length of the procedure to be captured. Comments Age is generally used when the patient reports an age at which the procedure was performed. Range is generally used when the patient reports an age range when the procedure was performed, such as sometime between 20-25 years old. dateTime supports a range of precision due to some procedures being reported as past procedures that might not have millisecond precision while other procedures performed and documented during the encounter might have more precise UTC timestamps with timezone. Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a workflow: Event.occurrence[x] w5: FiveWs.done[x] v2: OBR-7 rim: .effectiveTime
performedDateTime			dateTime	There are no (further) constraints on this element Data type dateTime
performedPeriod			Period	There are no (further) constraints on this element Data type Period
performedString			string	There are no (further) constraints on this element Data type string
performedAge			Age	There are no (further) constraints on this element Data type Age
performedRange			Range	There are no (further) constraints on this element Data type Range
recorder	Σ I	0..1	Reference(Patient \| RelatedPerson \| Practitioner \| PractitionerRole)	There are no (further) constraints on this element Element id Procedure.recorder Short description Who recorded the procedure Definition Individual who recorded the record and takes responsibility for its content. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Patient \| RelatedPerson \| Practitioner \| PractitionerRole) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) w5: FiveWs.author rim: .participation[typeCode=AUT].role
asserter	Σ I	0..1	Reference(Patient \| RelatedPerson \| Practitioner \| PractitionerRole)	There are no (further) constraints on this element Element id Procedure.asserter Short description Person who asserts this procedure Definition Individual who is making the procedure statement. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Patient \| RelatedPerson \| Practitioner \| PractitionerRole) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) w5: FiveWs.source rim: .participation[typeCode=INF].role
performer	Σ	0..*	BackboneElement	There are no (further) constraints on this element Element id Procedure.performer Short description The people who performed the procedure Definition Limited to "real" people rather than equipment. Data type BackboneElement Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a workflow: Event.performer rim: .participation[typeCode=PRF]
id		0..1	string	There are no (further) constraints on this element Element id Procedure.performer.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id Procedure.performer.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
modifierExtension	Σ ?! I	0..*	Extension	There are no (further) constraints on this element Element id Procedure.performer.modifierExtension Short description Extensions that cannot be ignored even if unrecognized Alternate names extensions, user content, modifiers Definition May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). Requirements Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
function	Σ	0..1	CodeableConcept	There are no (further) constraints on this element Element id Procedure.performer.function Short description Type of performance Definition Distinguishes the type of involvement of the performer in the procedure. For example, surgeon, anaesthetist, endoscopist. Requirements Allows disambiguation of the types of involvement of different performers. Comments Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. Data type CodeableConcept Binding A code that identifies the role of a performer of the procedure. ProcedurePerformerRoleCodes (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD workflow: Event.performer.function v2: Some combination of STF-18 / PRA-3 / PRT-4 / ROL-3 / ORC-12 / OBR-16 / PV1-7 / PV1-8 / PV1-9 / PV1-17 / OBX-25 rim: .functionCode
actor	Σ I	1..1	Reference(Practitioner \| PractitionerRole \| Organization \| Patient \| RelatedPerson \| Device)	There are no (further) constraints on this element Element id Procedure.performer.actor Short description The reference to the practitioner Definition The practitioner who was involved in the procedure. Requirements A reference to Device supports use cases, such as pacemakers. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Practitioner \| PractitionerRole \| Organization \| Patient \| RelatedPerson \| Device) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) workflow: Event.performer.actor w5: FiveWs.actor v2: ORC-19/PRT-5 rim: .role
onBehalfOf	I	0..1	Reference(Organization)	There are no (further) constraints on this element Element id Procedure.performer.onBehalfOf Short description Organization the device or practitioner was acting for Definition The organization the device or practitioner was acting on behalf of. Requirements Practitioners and Devices can be associated with multiple organizations. This element indicates which organization they were acting on behalf of when performing the action. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Organization) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) rim: .scoper
location	Σ I	0..1	Reference(Location)	There are no (further) constraints on this element Element id Procedure.location Short description Where the procedure happened Definition The location where the procedure actually happened. E.g. a newborn at home, a tracheostomy at a restaurant. Requirements Ties a procedure to where the records are likely kept. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Location) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) w5: FiveWs.where[x] rim: .participation[typeCode=LOC].role[classCode=SDLOC]
reasonCode	Σ	0..*	CodeableConcept	There are no (further) constraints on this element Element id Procedure.reasonCode Short description Coded reason procedure performed Definition The coded reason why the procedure was performed. This may be a coded entity of some type, or may simply be present as text. Comments Use Procedure.reasonCode when a code sufficiently describes the reason. Use Procedure.reasonReference when referencing a resource, which allows more information to be conveyed, such as onset date. Procedure.reasonCode and Procedure.reasonReference are not meant to be duplicative. For a single reason, either Procedure.reasonCode or Procedure.reasonReference can be used. Procedure.reasonCode may be a summary code, or Procedure.reasonReference may be used to reference a very precise definition of the reason using Condition \| Observation \| Procedure \| DiagnosticReport \| DocumentReference. Both Procedure.reasonCode and Procedure.reasonReference can be used if they are describing different reasons for the procedure. Data type CodeableConcept Binding A code that identifies the reason a procedure is required. ProcedureReasonCodes (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD workflow: Event.reasonCode w5: FiveWs.why[x] rim: .reasonCode
reasonReference	Σ I	0..*	Reference(Condition \| Observation \| Procedure \| DiagnosticReport \| DocumentReference)	There are no (further) constraints on this element Element id Procedure.reasonReference Short description The justification that the procedure was performed Definition The justification of why the procedure was performed. Comments It is possible for a procedure to be a reason (such as C-Section) for another procedure (such as an epidural). Other examples include endoscopy for dilatation and biopsy (a combination of diagnostic and therapeutic use). Use Procedure.reasonCode when a code sufficiently describes the reason. Use Procedure.reasonReference when referencing a resource, which allows more information to be conveyed, such as onset date. Procedure.reasonCode and Procedure.reasonReference are not meant to be duplicative. For a single reason, either Procedure.reasonCode or Procedure.reasonReference can be used. Procedure.reasonCode may be a summary code, or Procedure.reasonReference may be used to reference a very precise definition of the reason using Condition \| Observation \| Procedure \| DiagnosticReport \| DocumentReference. Both Procedure.reasonCode and Procedure.reasonReference can be used if they are describing different reasons for the procedure. Data type Reference(Condition \| Observation \| Procedure \| DiagnosticReport \| DocumentReference) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) workflow: Event.reasonReference w5: FiveWs.why[x] rim: .reasonCode
bodySite	Σ	0..*	CodeableConceptBinding	Element id Procedure.bodySite Short description Target body sites Definition Detailed and structured anatomical location information. Multiple locations are allowed - e.g. multiple punch biopsies of a lesion. Comments If the use case requires attributes from the BodySite resource (e.g. to identify and track separately) then use the standard extension procedure-targetbodystructure. Data type CodeableConcept Binding Codes describing anatomical locations. May include laterality. SNOMEDCTBodyStructures (preferred) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD v2: OBX-20 rim: .targetSiteCode
outcome	Σ	0..1	CodeableConcept	There are no (further) constraints on this element Element id Procedure.outcome Short description The result of procedure Definition The outcome of the procedure - did it resolve the reasons for the procedure being performed? Comments If outcome contains narrative text only, it can be captured using the CodeableConcept.text. Data type CodeableConcept Binding An outcome of a procedure - whether it was resolved or otherwise. ProcedureOutcomeCodes(SNOMEDCT) (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD rim: .outboundRelationship[typeCode=OUT].target.text
report	I	0..*	Reference(DiagnosticReport \| DocumentReference \| Composition)	There are no (further) constraints on this element Element id Procedure.report Short description Any report resulting from the procedure Definition This could be a histology result, pathology report, surgical report, etc. Comments There could potentially be multiple reports - e.g. if this was a procedure which took multiple biopsies resulting in a number of anatomical pathology reports. Data type Reference(DiagnosticReport \| DocumentReference \| Composition) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) rim: .inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN]
complication		0..*	CodeableConceptBinding	Element id Procedure.complication Short description Complication following the procedure Definition Any complications that occurred during the procedure, or in the immediate post-performance period. These are generally tracked separately from the notes, which will typically describe the procedure itself rather than any 'post procedure' issues. Comments If complications are only expressed by the narrative text, they can be captured using the CodeableConcept.text. Data type CodeableConcept Binding A code from the SNOMED Clinical Terminology UK with the expression (<404684003 \|Clinical finding\| OR <413350009 \|Finding with explicit context\| OR <272379006 \|Event\|). UKCoreConditionCode (preferred) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD rim: .outboundRelationship[typeCode=OUTC].target[classCode=OBS, code="complication", moodCode=EVN].value
complicationDetail	I	0..*	Reference(Condition)	There are no (further) constraints on this element Element id Procedure.complicationDetail Short description A condition that is a result of the procedure Definition Any complications that occurred during the procedure, or in the immediate post-performance period. Requirements This is used to document a condition that is a result of the procedure, not the condition that was the reason for the procedure. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Condition) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) rim: .outboundRelationship[typeCode=OUTC].target[classCode=OBS, code="complication", moodCode=EVN].value
followUp		0..*	CodeableConcept	There are no (further) constraints on this element Element id Procedure.followUp Short description Instructions for follow up Definition If the procedure required specific follow up - e.g. removal of sutures. The follow up may be represented as a simple note or could potentially be more complex, in which case the CarePlan resource can be used. Comments Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. Data type CodeableConcept Binding Specific follow up required for a procedure e.g. removal of sutures. ProcedureFollowUpCodes(SNOMEDCT) (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD rim: .outboundRelationship[typeCode=COMP].target[classCode=ACT, moodCode=INT].code
note		0..*	Annotation	There are no (further) constraints on this element Element id Procedure.note Short description Additional information about the procedure Definition Any other notes and comments about the procedure. Comments For systems that do not have structured annotations, they can simply communicate a single annotation with no author or time. This element may need to be included in narrative because of the potential for modifying information. Annotations SHOULD NOT be used to communicate "modifying" information that could be computable. (This is a SHOULD because enforcing user behavior is nearly impossible). Data type Annotation Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: N/A rim: Act workflow: Event.note v2: NTE rim: .inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code="annotation"].value
focalDevice		0..*	BackboneElement	There are no (further) constraints on this element Element id Procedure.focalDevice Short description Manipulated, implanted, or removed device Definition A device that is implanted, removed or otherwise manipulated (calibration, battery replacement, fitting a prosthesis, attaching a wound-vac, etc.) as a focal portion of the Procedure. Data type BackboneElement Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a rim: .participation[typeCode=DEV].role[classCode=MANU]
id		0..1	string	There are no (further) constraints on this element Element id Procedure.focalDevice.id Short description Unique id for inter-element referencing Definition Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces. Data type string Mappings rim: n/a
extension	I	0..*	Extension	There are no (further) constraints on this element Element id Procedure.focalDevice.extension Short description Additional content defined by implementations Alternate names extensions, user content Definition May be used to represent additional information that is not part of the basic definition of the element. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Sliced: Unordered, Open, by url(Value) Extensions are always sliced by (at least) url Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
modifierExtension	Σ ?! I	0..*	Extension	There are no (further) constraints on this element Element id Procedure.focalDevice.modifierExtension Short description Extensions that cannot be ignored even if unrecognized Alternate names extensions, user content, modifiers Definition May be used to represent additional information that is not part of the basic definition of the element and that modifies the understanding of the element in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself). Requirements Modifier extensions allow for extensions that cannot be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the definition of modifier extensions. Comments There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone. Data type Extension Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ext-1: Must have either extensions or value[x], not both `extension.exists() != value.exists()` Mappings rim: n/a rim: N/A
action		0..1	CodeableConceptBinding	There are no (further) constraints on this element Element id Procedure.focalDevice.action Short description Kind of change to device Definition The kind of change that happened to the device during the procedure. Comments Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination. Data type CodeableConcept Binding A kind of change that happened to the device during the procedure. ProcedureDeviceActionCodes (preferred) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD rim: .inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code="procedure device action"].value=:procedure device action codes
manipulated	I	1..1	Reference(Device)	There are no (further) constraints on this element Element id Procedure.focalDevice.manipulated Short description Device that was changed Definition The device that was manipulated (changed) during the procedure. Comments References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository. Data type Reference(Device) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) rim: .participation[typeCode=DEV].role[classCode=SDLOC]
usedReference	I	0..*	Reference(Device \| Medication \| Substance)	There are no (further) constraints on this element Element id Procedure.usedReference Short description Items used during procedure Definition Identifies medications, devices and any other substance used as part of the procedure. Requirements Used for tracking contamination, etc. Comments For devices actually implanted or removed, use Procedure.device. Data type Reference(Device \| Medication \| Substance) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` ref-1: SHALL have a contained resource if a local reference is provided `reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))` Mappings rim: n/a rim: The target of a resource reference is a RIM entry point (Act, Role, or Entity) rim: .participation[typeCode=DEV].role[classCode=MANU] or .participation[typeCode=CSM].role[classCode=ADMM] (for Medication or Substance)
usedCode		0..*	CodeableConcept	There are no (further) constraints on this element Element id Procedure.usedCode Short description Coded items used during the procedure Definition Identifies coded items that were used as part of the procedure. Comments For devices actually implanted or removed, use Procedure.device. Data type CodeableConcept Binding Codes describing items used during a procedure. FHIRDeviceTypes (example) Constraints ele-1: All FHIR elements must have a @value or children `hasValue() or (children().count() > id.count())` Mappings rim: n/a v2: CE/CNE/CWE rim: CD orim: fhir:CodeableConcept rdfs:subClassOf dt:CD rim: participation[typeCode=Dev].role[classCode=MANU]

FHIR	MDS	HL7v2
Procedure	Patient - Had transplant, Patient - Had transfusion, Is patient on TKI therapy, Insulin treated within 6 months of diagnosis, Is on Ig replacement	Presence of OBR segment with OBR-44 code for transplant/transfusion etc.
Procedure.performedDateTime	Patient - Fetal gestation (to determine termination date), Patient - Transplant date, Patient - Transfusion date	OBR-7
Procedure.code	Patient - Pregnancy type, Patient - Type of transplant, Patient - Type of transfusion, Neonatal hypoglycemia treatment details, Current exocrine pancreatic treatment	OBR segments with appropriate codes, OBR-44, OBR/RXA segments
Procedure.performedPeriod.start	Neonatal hypoglycemia treatment start date, Exocrine pancreatic treatment start date	OBR-7, RXA-3
Procedure.performedPeriod.end	Neonatal hypoglycemia treatment end date	OBR-8

Propose a change to UKCore-Procedure

extension:genomic-study-analysis

TBC. From the Genomic Reporting IG Genomic Study profile. Reference to the Genomic Study Analysis resource, detailing the analyses performed as part of genomic test.

"extension" : [
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-ext",
      "valueReference" : {
        "reference" : "Procedure/PGXGenomicStudyAnalysis"
      }
    }
  ],

Genomic Study Analysis extensions

TBC. From the Genomic Reporting IG Genomic Study Analysis profile. Various extensions covering the metadata related to a genomic test, e.g. regions studied, change types tested for etc. For the full list of extensions, please see the linked profile page.

Use of the profile and its extensions is pending further discovery of the data standards required for Genomic Reporting in the UK.

"extension" : [
    {
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build",
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA26806-2",
            "display" : "GRCh38"
          }
        ]
      }
    },
    {
      "extension" : [
        {
          "url" : "sequencing-coverage",
          "valueQuantity" : {
            "value" : 100
          }
        }
      ],
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics"
    },
    {
      "extension" : [
        {
          "url" : "description",
          "valueString" : "protein-coding and exon-splicing regions"
        },
        {
          "url" : "studied",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://www.genenames.org",
                "code" : "HGNC:2621",
                "display" : "CYP2C19"
              }
            ]
          }
        },
        {
          "url" : "studied",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://www.genenames.org",
                "code" : "HGNC:2623",
                "display" : "CYP2C9"
              }
            ]
          }
        },
        {
          "url" : "studied",
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://www.genenames.org",
                "code" : "HGNC:23663",
                "display" : "VKORC1"
              }
            ]
          }
        }
      ],
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions"
    }
  ],

status

Status SHALL use the codes recommended in the base Procedure resource, appropriately tagging procedures as having been completed or in-progress etc. depending on the actual status of the procedure.

"status": "completed",

code

SHALL be present. SNOMED CT coding is preferred, though alternative codings MAY be provided subject to review of the Coding system by the NHS England Genomics Unit.

For the Genomic Study profile, expected to be from the Genomic Study Type ValueSet

"code": {
        "coding":  [
            {
                "system": "http://snomed.info/sct",
                "code": "23719005",
                "display": "Transplantation of bone marrow"
            }
        ]
    },

subject

SHALL be present. Reference to the associated Patient. This MAY be through a resource reference if the ID on the central service is known (or provided within the transaction bundle) or through NHS number where this is known and has been traced through PDS.

"subject": {
        "reference": "Patient/Patient-MeirLieberman-Example",
        "identifier": {
            "system": "https://fhir.nhs.uk/Id/nhs-number",
            "value": "9449307873"
        }
    },

performed[x]

performed SHOULD be provided wherever possible, using the appropriate data type, to aid in interpretation of Genomic test results.

"performedDateTime": "2020-01-19"